Draft Genome Sequence of Anammox Bacterium “Candidatus
Scalindua brodae,” Obtained Using Differential Coverage Binning of
Sequencing Data from Two Reactor Enrichments
Daan R. Speth,aLina Russ,aBoran Kartal,aHuub J. M. op den Camp,aBas E. Dutilh,b,c,dMike S. M. Jettena,e
Ecological Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlandsa; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlandsb; Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlandsc; Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazild; Department of Biotechnology, Delft University of Technology, Delft, The Netherlandse
We present the draft genome of anammox bacterium “Candidatus Scalindua brodae,” which at 282 contigs is a major improve-ment over the highly fragimprove-mented genome assembly of related species “Ca. Scalindua profunda” (1,580 contigs) which was previ-ously published.
Received 27 November 2014 Accepted 1 December 2014 Published 8 January 2015
Citation Speth DR, Russ L, Kartal B, op den Camp HJM, Dutilh BE, Jetten MSM. 2015. Draft genome sequence of anammox bacterium “Candidatus Scalindua brodae,” obtained
using differential coverage binning of sequencing data from two reactor enrichments. Genome Announc. 3(1):e01415-14. doi:10.1128/genomeA.01415-14.
Copyright © 2015 Speth et al. This is an open-access article distributed under the terms of theCreative Commons Attribution 3.0 Unported license.
Address correspondence to Daan R.Speth, d.speth@science.ru.nl.
A
nammox bacteria are major players in the global nitrogen cycle, capable of anaerobically oxidizing ammonium to dini-trogen gas, using nitrite as the electron acceptor (1). All currently known anammox bacteria form the monophyletic orderBroca-diales within the phylum Planctomycetes (2). Until now, draft ge-nomes of four anammox species have been reported (3–6). The genome assemblies of “Candidatus Kuenenia stuttgartiensis” and “Ca. Jettenia caeni” are in 5 and 4 contigs, respectively, whereas the draft genome of “Ca. Brocadia fulgida” (411 contigs) is frag-mented and the “Ca. Scalindua profunda” draft genome (1,580 contigs) is highly fragmented.
Despite advances in culturing techniques, no pure culture of anammox bacteria exists. This restricts genome-sequencing ef-forts to metagenomic sequencing and binning (7, 8). Here we employed a differential coverage binning approach (9) to increase the confidence of the binning result. We combined sequencing data from Russ et al. (10) with sequencing data from the enrich-ment culture used as seed for the experienrich-mental reactor described in Russ et al. (10). The raw sequence data are available in DDBJ/EMBL/Genbank under accession no. ERX443234 and SRX719339. DNA isolation and sequencing of both enrichments was performed as described previously, using the Powersoil DNA isolation kit (Mo-Bio, Carlsbad, CA, USA) according to the man-ufacturer’s instructions and the Ion Torrent 200 bp workflow (10).
All data were co-assembled using the CLC genomics workbench (v7.0.4, CLCbio, Arhus, Denmark) de novo assembler, using word size 35 and bubble size 5,000. The obtained contigs were binned with a workflow modified from Albertsen et al. (9) using custom scripts available at http://www.github.com/dspeth/bioinfo_scripts. The binned “Ca. Scalindua brodae” genome consisted of 282 contigs and was annotated using Prokka 1.10 (11) followed by manual curation. Frameshifts were corrected using the CLC genomics workbench (v7.0.4, CLCbio, Arhus, Denmark) and a Perl script available athttp://www.github.com/dspeth/bioinfo_scripts. The
completeness (⬎92%) of the draft genome was assessed using CheckM (12). The contigs have a total length of 4.1 Mb, average G⫹C content of 39.6%, and encode 4,016 genes, 39 tRNAs, and 1 rRNA operon.
Hydrazine is a key intermediate in anammox metabolism and the enzymes involved in its turnover are unique to anammox bac-teria. The fusion of subunits B and C of the hydrazine synthase operon (hzsBC), earlier reported for “Ca. Scalindua profunda” (6), was confirmed and additionally the fused genes seemed to have undergone duplication. The presence of two copies of hzsBC prohibited resolving their genomic location without mate pair information. As a result, the hydrazine synthase BC gene is present on a separate contig. The hydrazine dehydrogenase is also present in two copies, but their genomic location could be resolved based on sequence difference.
Nucleotide sequence accession numbers. This whole-genome
shotgun project has been deposited at DDBJ/EMBL/GenBank un-der the accession no.JRYO00000000. The version described in this paper is the first version, JRYO01000000.
ACKNOWLEDGMENTS
The work was supported by European Research Council grant 232937 to M.S.M.J. and L.R., NWO VENI grant 863.11.003 to B.K., and BE-Basic grant fp07-2F to D.R.S.
REFERENCES
1. Kartal B, Maalcke WJ, de Almeida NM, Cirpus I, Gloerich J, Geerts W,
Op den Camp HJM, Harhangi HR, Janssen-Megens EM, Francoijs K-J, Stunnenberg HG, Keltjens JT, Jetten MSM, Strous M. 2011. Molecular
mechanism of anaerobic ammonium oxidation. Nature 479:127–130.
http://dx.doi.org/10.1038/nature10453.
2. Jetten MSM, Op den Camp HJ, Kuenen JG, Strous M. 2010. Description of the order Brocadiales, p 596 – 603. In Krieg NR, Staley JT, Hedlund BP, Paster BJ, Ward N, Ludwig W, Whitman WB (ed), Bergey’s manual of systematic bacteriology, vol 4. Springer Verlag, Heidelberg, Germany. 3. Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW,
Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten
crossmark
Genome Announcements
January/February 2015 Volume 3 Issue 1 e01415-14 genomea.asm.org 1
on September 9, 2015 by BIBLIOTHEEK TU DELFT
http://genomea.asm.org/
N, Vallenet D, Segurens B, Schenowitz-Truong C, Médigue C, Col-lingro A, Snel B, Dutilh BE, Op den Camp HJM, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frish-man D, Huynen MA, Mewes H-W, Weissenbach J, Jetten MSM, Wag-ner M, Le Paslier D. 2006. Deciphering the evolution and metabolism of
an anammox bacterium from a community genome. Nature 440: 790 –794.http://dx.doi.org/10.1038/nature04647.
4. Hira D, Toh H, Migita CT, Okubo H, Nishiyama T, Hattori M,
Furukawa K, Fujii T. 2012. Anammox organism KSU-1 expresses a
NirK-type copper-containing nitrite reductase instead of a NirS-NirK-type with cyto-chrome cd1. FEBS Lett 586:1658 –1663.http://dx.doi.org/10.1016/
j.feb-slet.2012.04.041.
5. Ferousi C, Speth DR, Reimann J, Op den Camp HJ, Allen JW, Keltjens
JT, Jetten MS. 2013. Identification of the type II cytochrome c maturation
pathway in anammox bacteria by comparative genomics. BMC Microbiol
13:265.http://dx.doi.org/10.1186/1471-2180-13-265.
6. van de Vossenberg J, Woebken D, Maalcke WJ, Wessels HJCT, Dutilh
BE, Kartal B, Janssen-Megens EM, Roeselers G, Yan J, Speth D, Glo-erich J, Geerts W, van der Biezen E, Pluk W, Francoijs K-J, Russ L, Lam P, Malfatti SA, Tringe SG, Haaijer SCM, Op den Camp HJM, Stun-nenberg HG, Amann R, Kuypers MMM, Jetten MSM. 2013. The
met-agenome of the marine anammox bacterium “Candidatus Scalindua
pro-funda” illustrates the versatility of this globally important nitrogen cycle bacterium. Environ Microbiol 15:1275–1289.http://dx.doi.org/10.1111/ j.1462-2920.2012.02774.x.
7. van der Star WRL, Miclea AI, van Dongen UGJM, Muyzer G,
Picio-reanu C, van Loosdrecht MCM. 2008. The membrane bioreactor: A
novel tool to grow anammox bacteria as free cells. Biotechnol Bioeng
101:286 –294.http://dx.doi.org/10.1002/bit.21891.
8. Sharon I, Banfield JF. 2013. Genomes from metagenomics. Science 342: 1057–1058.http://dx.doi.org/10.1126/science.1247023.
9. Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW,
Nielsen PH. 2013. Genome sequences of rare, uncultured bacteria
ob-tained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31:533–538.http://dx.doi.org/10.1038/nbt.2579.
10. Russ L, Speth DR, Jetten MSM, Op den Camp HJM, Kartal B. 2014. Interactions between anaerobic ammonium and sulfur-oxidizing bacteria in a laboratory scale model system. Environ Microbiol 16:3487–3498.
http://dx.doi.org/10.1111/1462-2920.12487.
11. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinfor-matics 30:2068 –2069.http://dx.doi.org/10.1093/bioinformatics/btu153. 12. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW.
2014. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells and metagenomes. PeerJ PrePrints 2:e554v1. doi:
http://dx.doi.org/10.7287/peerj.preprints.554v1.
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